[CP2K:3137] Metadynamics Bug report in colvar: DISTANCE

Teodoro Laino teodor... at gmail.com
Thu Mar 10 15:48:50 CET 2011


As an add-on:

you can have a topology even for QM run: you can provide it with a PSF, let CP2K compute it or via AMBER topology, etc...
It only handles the definition of the molecule, since there is no FF involved.. but still could be quite useful for analysis.

Without knowing your input file it is hard to tell if you enabled it by chance or you used the defaults.
If you used the defaults than the topology built is such that any atom is a molecule.
If this is true (as it appears from the short output sent in the message) than just the activation of the
keyword: INTERMOLECULAR in &COLLECTIVE should fix your problem.

Remember that constraint must be converted in a restraint - constraints and geo opts do not work together in CP2K.

Cheers
Teo


On Mar 10, 2011, at 3:33 PM, Bernd Ensing wrote:

> Dear people,
> 
> I would like to perform a constrained geometry optimazation with
> Quickstep. I have defined a torsion collective variable in the &SUBSYS
> part of the input:
> ===================================================================
>    &COLVAR
>      &TORSION
>        ATOMS 1 2 3 4
>      &END
>    &END
> ===================================================================
> 
> and a constraint definition in the &MOTION section:
> 
> ===================================================================
>  &CONSTRAINT
>    &COLLECTIVE
>      TARGET -1.3788
>      MOLECULE 1
>      COLVAR 1
>    &END COLLECTIVE
>  &END CONSTRAINT
> ===================================================================
> 
> but for some reason I get the following error at the end of the output:
> 
> ===================================================================
>         ----------------------------------------------------------------------
> COLVARS| COLVAR INPUT INDEX:        1
> COLVARS| TORSION       >>> ATOMS:                     1       2       3       4
>          ----------------------------------------------------------------------
> 
> CELL_TOP| Volume [angstrom^3]:                                         8000.000
> CELL_TOP| Vector a [angstrom    20.000     0.000     0.000    |a| =      20.000
> CELL_TOP| Vector b [angstrom     0.000    20.000     0.000    |b| =      20.000
> CELL_TOP| Vector c [angstrom     0.000     0.000    20.000    |c| =      20.000
> CELL_TOP| Angle (b,c), alpha [degree]:                                   90.000
> CELL_TOP| Angle (a,c), beta  [degree]:                                   90.000
> CELL_TOP| Angle (a,b), gamma [degree]:                                   90.000
>    |  Error in constraints setup!
>    |  A constraint has been defined for a molecule type
>    |   but the atoms specified in the constraint and the atoms defined for
>    |   the molecule DO NOT match!
>    |  This could be very probable due to a wrong connectivity, or an error
>    |   in the constraint specification in the input file.
>    |   Please check it carefully!
>    |  Error in constraints setup!
> GENERATE|  Preliminary Number of Bonds generated:                             0
> GENERATE|  Achieved consistency in connectivity generation.
> GENERATE|  Number of Bonds generated:                                         0
> GENERATE|  Preliminary Number of Bends generated:                             0
> GENERATE|  Number of Bends generated:                                         0
> GENERATE|  Number of UB generated:                                            0
> GENERATE|  Preliminary Number of Torsions generated:                          0
> GENERATE|  Number of Torsions generated:                                      0
> GENERATE|  Number of Impropers generated:                                     0
> GENERATE|  Number of 1-4 interactions generated:                              0
>    |  Error in constraints setup!
>    |  A constraint has been defined for a molecule type
>    |   but the atoms specified in the constraint and the atoms defined for
>    |   the molecule DO NOT match!
>    |  This could be very probable due to a wrong connectivity, or an error
>    |   in the constraint specification in the input file.
>    |   Please check it carefully!
> *
> *** 15:06:36 ERRORL2 in topology_constraint_util:setup_lcolv processor     ***
> ***   0  err=-300  condition FAILED at line 1201                           ***
> *
> 
> ===== Routine Calling Stack =====
> 
>            4 topology_constraint_pack
>            3 topology_control
>            2 quickstep_create_force_env
>            1 CP2K
> CP2K| condition FAILED at line 1201
> CP2K| Abnormal program termination, stopped by process number 0
> ===================================================================
> 
> 
> What I understand from this error message is that it compares the
> atoms in the torsion collective variable with the atoms in the
> topology, which then don't seem to match. Mind you that this is not a
> classical forcefield run, so I don't quite understand what is meant
> with a topology.
> In any case, there are more than 4 atoms in the system, so specifying
> atoms 1, 2, 3, 4 in the collective variable should be fine, I thought.
> Does anybody understand this error and knows how to fix it?
> 
> many thanks in advance,
> 
> Bernd Ensing
> 
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